r-gdr: init

BioArchLinux/r-gdr/PKGBUILD

@@ -0,0 +1,53 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=gDR
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Umbrella package for R packages in the gDR suite"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-gdrcore
+  r-gdrimport
+  r-gdrutils
+)
+checkdepends=(
+  r-gdrtestdata
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-bumpymatrix
+  r-futile.logger
+  r-gdrstyle
+  r-gdrtestdata
+  r-kableextra
+  r-knitr
+  r-markdown
+  r-purrr
+  r-rmarkdown
+  r-summarizedexperiment
+  r-testthat
+  r-yaml
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('abefb906e5c9ec014a443b0367844ac9')
+sha256sums=('a9d1ebab30108c72a544a933c49264aad4435ae79e01f478ee6dd8d07c93e57d')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-gdr/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-gdr/lilac.yaml

@@ -0,0 +1,17 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-gdrcore
+- r-gdrimport
+- r-gdrutils
+repo_makedepends:
+- r-gdrtestdata
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: gDR
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-gdrcore/PKGBUILD

@@ -0,0 +1,60 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=gDRcore
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Processing functions and interface to process and analyze drug dose-response data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-biocparallel
+  r-bumpymatrix
+  r-checkmate
+  r-data.table
+  r-futile.logger
+  r-gdrutils
+  r-multiassayexperiment
+  r-purrr
+  r-s4vectors
+  r-stringr
+  r-summarizedexperiment
+)
+checkdepends=(
+  r-gdrimport
+  r-gdrtestdata
+  r-qs
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-gdrimport
+  r-gdrstyle
+  r-gdrtestdata
+  r-iranges
+  r-knitr
+  r-pkgbuild
+  r-qs
+  r-testthat
+  r-yaml
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('76f729e9fce669107120d0ec73c32bfc')
+sha256sums=('8eb4527eac26056bed31d02e29703623c11f69505c4224674abe7fa8b6bf05a1')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-gdrcore/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-gdrcore/lilac.yaml

@@ -0,0 +1,27 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocparallel
+- r-bumpymatrix
+- r-checkmate
+- r-data.table
+- r-futile.logger
+- r-gdrutils
+- r-multiassayexperiment
+- r-purrr
+- r-s4vectors
+- r-stringr
+- r-summarizedexperiment
+repo_makedepends:
+- r-gdrimport
+- r-gdrtestdata
+- r-qs
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: gDRcore
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-gdrimport/PKGBUILD

@@ -0,0 +1,63 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=gDRimport
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Package for handling the import of dose-response data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-assertthat
+  r-bumpymatrix
+  r-checkmate
+  r-coregx
+  r-data.table
+  r-futile.logger
+  r-gdrutils
+  r-magrittr
+  r-multiassayexperiment
+  r-openxlsx
+  r-pharmacogx
+  r-readxl
+  r-rio
+  r-s4vectors
+  r-stringi
+  r-summarizedexperiment
+  r-tibble
+  r-xml
+  r-yaml
+)
+checkdepends=(
+  r-qs
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-gdrstyle
+  r-gdrtestdata
+  r-knitr
+  r-purrr
+  r-qs
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('0390ee6a16f21624044bc509ebdbabd1')
+sha256sums=('469a7e74c8478d9f5d7a79ca0365f3554d9a784d09b4e6ca73e3a9c10cb29ed3')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-gdrimport/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-gdrimport/lilac.yaml

@@ -0,0 +1,33 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-assertthat
+- r-bumpymatrix
+- r-checkmate
+- r-coregx
+- r-data.table
+- r-futile.logger
+- r-gdrutils
+- r-magrittr
+- r-multiassayexperiment
+- r-openxlsx
+- r-pharmacogx
+- r-readxl
+- r-rio
+- r-s4vectors
+- r-stringi
+- r-summarizedexperiment
+- r-tibble
+- r-xml
+- r-yaml
+repo_makedepends:
+- r-qs
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: gDRimport
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-gdrtestdata/PKGBUILD

@@ -0,0 +1,46 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=gDRtestData
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="gDRtestData - R data package with testing dose reponse data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-checkmate
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-data.table
+  r-gdrstyle
+  r-knitr
+  r-qs
+  r-reshape2
+  r-rmarkdown
+  r-summarizedexperiment
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('8de3dea2673f0e7dc9412e36da2c4f9d')
+sha256sums=('19b06102d2720e5d2b423a98b7075fecf22b7769314ed64c6379c3c0f6f5995f')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-gdrtestdata/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-gdrtestdata/lilac.yaml

@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-checkmate
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: gDRtestData
+  repo: bioc-data-experiment
+  md5: true
+- alias: r

BioArchLinux/r-gdrutils/PKGBUILD

@@ -0,0 +1,65 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=gDRutils
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="A package with helper functions for processing drug response data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-biocparallel
+  r-bumpymatrix
+  r-checkmate
+  r-data.table
+  r-drc
+  r-jsonlite
+  r-jsonvalidate
+  r-magrittr
+  r-multiassayexperiment
+  r-s4vectors
+  r-stringr
+  r-summarizedexperiment
+)
+checkdepends=(
+  r-gdrtestdata
+  r-qs
+  r-testthat
+  r-yaml
+)
+optdepends=(
+  r-biocmanager
+  r-biocstyle
+  r-futile.logger
+  r-gdrstyle
+  r-gdrtestdata
+  r-iranges
+  r-knitr
+  r-lintr
+  r-purrr
+  r-qs
+  r-rcmdcheck
+  r-rmarkdown
+  r-testthat
+  r-yaml
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('fdf71802bbd5967b163447eda2fe37ef')
+sha256sums=('b06bd1bb0843ff8bc2137f207a1d07e30ebb477c8e9957acc912f689bf19f4f3')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-gdrutils/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-gdrutils/lilac.yaml

@@ -0,0 +1,28 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocparallel
+- r-bumpymatrix
+- r-checkmate
+- r-data.table
+- r-drc
+- r-jsonlite
+- r-jsonvalidate
+- r-magrittr
+- r-multiassayexperiment
+- r-s4vectors
+- r-stringr
+- r-summarizedexperiment
+repo_makedepends:
+- r-gdrtestdata
+- r-qs
+- r-testthat
+- r-yaml
+update_on:
+- source: rpkgs
+  pkgname: gDRutils
+  repo: bioc
+  md5: true
+- alias: r